There are no releases available for this repository. The content is, therefore, likely still under development and not production ready. Use at own risk!

A pipeline that tries to improve your assembly.

1. Takes your current assembly
2. Indexes it
3. Maps reads back to it
4. Extracts the reads from the resulting bam file
5. Constructs a new assembly using the extracted reads.

Usage

In order to run the complete multisample pipeline, you can run ReAssembly.wdl using Cromwell:

java -jar cromwell-<version>.jar run -i inputs.json ReAssembly.wdl

The inputs JSON can be generated using WOMtools as described in the WOMtools documentation. Note that not some inputs should not be used! See this page for more information.

The primary inputs are described below, additional inputs (such as precommands and JAR paths) are available. Please use the above mentioned WOMtools command to see all available inputs.

field	type	default
inputAssembly	File		The assembly which is to be reassembled.
outputDir	String		The output directory.
read1	File		The first end FASTQ files.
read2	File?		The second-end FASTQ files.

All inputs have to be preceded by ReAssembly.. Type is indicated according to the WDL data types: File should be indicators of file location (a string in JSON). Types ending in ? indicate the input is optional, types ending in + indicate they require at least one element.

Output

This pipeline will produce a new assembly, consisting of a scaffolds file and contigs file.

Contact

For any question related to this pipeline, please use the github issue tracker or contact the SASC team directly at: sasc@lumc.nl.